Hi Ila,
if the slice is a closed polyline, you should be able to use the 'Cover Loops' tool available in the 'Wire Tools' folder in the top panel to create a filled 2D section. Watch out that when you create a slice of some anatomical entities, such as the white or gray matter, you extract two slices, one for the internal and one for the internal regions. They are collected in only one slice entity, but you can separate them using the boolean operations.
Please let us know if that worked.